The Red Hunter
by bunji the wolf
Summary: While forming her team to battle the Collectors, Shepard is being hunted down by a armored being she calls the Hunter. It will stop at nothing to end Shepard's life but however, Shepard is not alone upon the battle to save the Galaxy as a new ally joins the battle! Naruto X Mass Effect, Naruto X Fem Shepard X Harem
1. Chapter 1

**Don't own the Naruto series or the Mass Effect series**

**Hello everyone Bunji the wolf here, yes, yes I know a new story, while writer block still got me for my other fics so deal with it! Well I had in idea in store for a long time. For about three months and half now, anyway this is Naruto X Fem Shepard-with slightly harem for Naruto-anyway talk more later enjoy everyone!**

**Also I like to thanks Xager-the-Chaos-King for helping me out for betaing this chapter.**

**Chapter I-The Hunter**

This the story of two souls that have died in battle, as each of them have lived their lives well and fought and defeated enemies that simply nearly unstoppable. But however fate has different plans for these two souls.

Shortly after defeating the Reapers that was known and feared as Sovereign, Commander Jane Shepard and her crew search through the endless stars of space for more answer for more clues to discover if the threat of the Reapers were true.

However Shepard and her crew were attacked by an unknown giant space ship that destroyed their ship the Normandy and ended the life of Shepard.

However there was a being that wanted to prove death was just an illusion and was desire to bring back the dead commander from the grave.

Our story begins here.

**Unknown Location:**

A large black ship fly through ship but shortly upon reaching a large space station.

"Now reaching destination, "The ship A.I spoke.

"Beware this location is heavily guarded. They will use their machines to stop you."

The man shook his head for a moment. The man stood up from his chair as he opened his arms and held them out wide as his body glow a bright greenish red color. Green lines glowed along with red glowing lines.

The armored man's ship flew to a large space station as it parked in the docking bay. As the ship door open the man looked around. The man was now in armor. His was six feet tall, and the armor the armored male wore was crimson from head to toe. There were dark blue lines coming from the neck of the suited armor that reached up to the helmet. The helmet was a much darker crimson color close to the color of thick blood. The helmet had a human likeliest in it, having an orange, V-shaped visor. The mouth of the helmet had two small breathing pads on each cheek. The hands were claws rather than hands. The right hand changed into a large buster gun while the left hand changed into a large glowing crystal wrist-blade.

The armored man notice the camera had focused on him. He easily shot down the security camera.

The armored man looked to see to his right a group of machine droids were coming towards him holding guns. The man held his right palm and smashed it on the floor as a green net line reached out to the machine hacking their systems.

"Find Shepard, kill everyone else." The voice of ship's A.I spoke the orders as they were given out to the droids, the armored man touched the wall while walking spreading his virus through the system.

The armored man made his way into the space station that held Jane Shepard. As the sound of gunfire and screams were heard but became quickly fell silent as the sound of loud of calm footsteps were soon heard echoing through the halls.

**Somewhere on the Space Station:**

"Shepard, Shepard, Shepard please wake up." The voice of a woman was heard.

"Shepard if you can hear me please wake up. Your life is in danger, you must wake up. I know you're still sore but you've got to get up and move. Shepard!" The woman's voice was loud as it woken the once slumbering form of the formerly dead commander.

Jane Shepard opened her eyes for the first time long since she was killed by the explosion that launched her into Outer space over Alchera. Jane found herself on a table, clothed and alive. She wasn't sure how it was even possible she was even alive at all, but right now she was alive and she needed to get out of here.

Jane couldn't shake away the headache she was having. Jane saw a nearby mirror to her right, seeing her beautiful short blood color red hair. Jane Shepard always had beautiful rare type of eyes heterochromic, red and green eyes they were.

Jane saw a nearby locker and went over to the locker. She opens the locker and found a pair of armor that fitted her shapely form perfectly. The armor was black, with red lines on the shoulder pad with the N7 emblem on the right breast plate. Jane took the armor and found a handgun within the locker, however the gun's ammo was empty.

Jane frowned at the sight of holding an empty gun. She felt naked. _'I need ammo' _she thought to herself. It didn't feel right holding a gun with no ammo to display.

Suddenly Jane heard the sound of screaming nearby. _'Just my rotten luck.'_ She thought.

Jane exited the room and found herself within an empty hallway. Jane saw a trail of blood on the floor that went from one room to another. Jane didn't like the looks of this and travelled along the left pathway, rather the right. Jane made her way throughout the space station only to find the corpses of the staff and crew members of the station strewn about the place. Jane entered a hallway where she saw a glass window. On the other side of the window she saw three men aiming their guns at what appears to be an armored being. Jane wasn't sure if it was a man or woman she saw.

"There it is, kill it. We have to protect Shepard." One of the men said. The three men opened fire on the armored being, however their guns did no damage to the being's armor, as their bullets simply bounced off the carapace. When they were out of ammo, the armored being simply tilted its head, as if it was waiting for them to finish. Seeing them growling at it, the armored humanoid aimed its arm cannon at them, and with one shot their blood covered the glass window.

Shepard couldn't believe what she just saw. She could hear the sound of footsteps. The armored being wiped the blood off the window and stare at Jane. Jane gasp as her heart raced suddenly. But however the armored being did nothing just stare.

Jane wondered _'Can it see me?'_. Unbeknownst to the both of them, the glass window was actually a one-way mirror. Only Jane could see what was happening on the other side. Suddenly smoke streamed out from the cheeks of the armored being. The armored being turned around and walk as the sound of its footsteps were heard throughout the empty room.

Jane left the hallway quickly before that thing even had a chance of finding her. Jane Shepard didn't know why, but when she was staring at the armored being, she felt a rare emotion: fear. She felt its powerful stare still gazing upon her, it felt wrong and lifeless. She couldn't shake the feeling it knew where she was behind that glass.

After traveling alone through the space station, Jane finally found ammo in a room. The room was small, as it turned out the room was the weapon storage room. Many of the stored weapons were missing. There one weapon still around, Jane smiled upon what she found still around.

A Grenade launcher. Smirking evilly, Jane took it and added it to her firearms. Jane left the room soon after claiming the new weapon. While entering a new area of the station, Jane encounter robots that once worked for the station but were now killing anyone or anything in their view.

They turn their sights on Jane and just before they even had the chance to aim, Jane shot their heads off with her handgun. After disposing of the robots, Jane began to panic when she heard the familiar, terrifying sound of footsteps drawing nearer.

Jane took cover behind the corner of the wall. Jane listen as the footsteps grew louder with each echoing step. The armored being was close by. Jane slowly and quietly pulled her grenade launcher off her back, and loaded it. Jane shut her eyes and silenced her breath, as the being was near.

The armored being looked around; it couldn't see Jane, as Jane had hidden herself in the shadow of the corner. Jane prayed whatever it was didn't see her. Jane slowly opened her eyes as her green eyes stare at the being.

It walked near a room where there was fuel tank right beside it. Jane took her chance and knew what to do now. Jane quickly jumped out from the shadow and rolled to the right and just when the armored being saw her, Jane pulled the trigger as the large round of the grenade launcher shot at the being as it send the being into the room.

Jane ran away and took corner at the corner from the room as the explosion went off. The sound of rumble falling was heard.

Jane sighed with relief as she peeked around the corner to see nothing but fire and debris lying around with no remains of her unknown guest. Jane smirked proudly and left the area as she made her way into the heart of the station, hoping to find someone alive or at least a way off this damn station.

**Few minutes later:**

Jane was able to meet two still living human beings. Lady Luck started to shine on Commander Jane Shepard. The two humans were two men. One was dark skin and the other was light skin, and both men were surprised to see Jane by the shock look on their faces.

"Shepard! You're alive?" One of them said with a shocked voice.

"Do I know you two? And what do you fucking mean I'm alive?" Jane stared at the two.

"Never mind him; it's good to see you alive and well Commander. I'm Jacob Taylor and this is Wilson." The dark skinned man introduced himself and Wilson to Jane. Jane continued to stare at them.

"Is something wrong?" Wilson asked Jane. Shepard shook her head as she broke her stare.

"What is this place? How did I end up here? I can see you two work for Cerberus." Jane frowned as she noticed Cerberus's symbol on the shoulder of their shirts.

Jacob was the first to sigh at this.

"We know your past encounter with Cerberus was…" Jacob paused only for Jane to finish what he started.

"A pain in the ass ride full of murderers, sickos and psychopaths?" Jane said with a contemptuous glare.

"Whatever you see Cerberus as. Know this, Cerberus brought you back Shepard. You were dead for two years and we brought you back from the dead." Wilson told Jane. Jane's green eyes opened wide in shock.

"And why would Cerberus do something like that? Last time I check Cerberus wanted me DEAD!" Jane remember her and crew stopped Cerberus many times in the past, destroying their plans, stopping sick and twisted experiments and many other things.

"Times change, Commander. Let's leave it at that shall we?" Jacob said to Jane, but Jane folded her arms over her ample chest. Jacob knew Shepard wanted some answers.

"I'll fill you in once we get out of here. I promise." Jacob told Jane. Jane let out a disappointed sigh but gave in with a nod.

"Fine! I'm sick of this place already, with the bodies and the robots and that thing." Jane mumbled on the last part.

"Huh?" The two men said together.

"Never mind, let's get out of here." Jane shook her head.

"But first thing first, do you have medi-gel on you? I got shot and I need it bad or I'll bleed out." Wilson said.

"You're telling me now?" Jane sighed.

"There should be some gel right in some the boxes over there." Jacob pointed behind Jane, as the red head went over to the boxes.

"Hurry up will ya!" Wilson yelled.

Jane rolled her eyes as she wanted to leave this guy to bleed out being with Cerberus. But she needed the two as they were the only ones around still alive.

"Found it." She said.

"About damn time!" Wilson groaned.

_'Keep that up and another bullet to the leg is all you'll get.'_ The red head thought.

After fixing up Wilson with some medi-gel, the three travelled together to the docking bay, where they hoped to find a way off the station.

"Wilson wait, we have to make sure if everyone got off this place. Miranda could be still around looking for us or for Shepard?" Jacob said to the man, but Wilson turned away without a second thought.

"Miranda Lawson, she could be somewhere dead like the others. There's no way she could survive, in C deck the machines were all over the place. I doubt she survived, beside Shepard is alive that was our job, remember Jacob?" Wilson said.

"Wilson," Jacob said with an angry glare.

"Miranda Lawson, who's that?" Jane asked.

"She was the one who was head of the project of bringing you back. It was called Project Lazarus." Jacob explained to Jane.

"Interesting name for an experiment to bring someone back from the dead." Jane said with a small chuckle.

"Anyway even if Miranda is alive, there's no way she can make it to us. Most of the bridge and area are completely destroyed!" Wilson went to the locked door, and unlocked it. As the doors open, standing there on the other side of the door was someone Wilson didn't plan on seeing again.

"Miranda you're…you're." Wilson said with a shock voice.

Bang!

Wilson dropped to the floor after being shot once in the chest.

"Alive?" Miranda said with a displeased frown.

Jane had her eyes on the woman before her, staring at the woman from head to toe, as this woman was Miranda Lawson. Her voice was very familiar to Jane's ears. Miranda's appearance slightly bothered Jane. Miranda had a young appearance of her beauty, Jane wouldn't lie Miranda was beautiful. Miranda's wore a skin tight white outfit. Miranda's breasts were just a bit bigger than Jane's, Jane's eyes lower down to see Miranda's hips were curvy and perfect as her thighs were large but not too large giving her a perfect size.

_'She's like a freaking doll, perfect in size. I bet I can put her in a box and call her-'_ but however Jane's thought was cut short when Miranda spoke to Jane.

"Shepard, are you okay?" She asked.

"Yes, I'm fine. Just bit surprise you shot him without questioning him." Jane looked down at Wilson's corpse.

"Wilson betrayed us and paid the price. It was simple to do." Miranda said.

"I take it you're going to take me away from this place into another Cerberus base? If so I want answers. Why would Cerberus bring me back from the fucking dead? Do they need someone to win a fucking beauty pageant or something?" Jane glared at Miranda but Miranda simply turned her attention to Jacob.

"Jacob I should've known you would have told the commander." Lawson sighed.

"Lying to the commander will get us nowhere." Jacob said truthfully.

"Fine, if there any questions before we go commander?" Miranda asked Jane with a sigh.

"The questions can wait. As of right now I want off this station. I have had enough of this place for a life time." Jane said with an edgy look.

"Or two in your case Shepard." Miranda said as either of them chuckle at the dark humor.

Miranda Lawson, Jacob Taylor and Jane Shepard escape the space station by using the remaining ships that was docked on the station. As they left the space station, Jane looked outside of the window as her gaze was fixed on the space station.

_'I wonder if I killed it?'_ Her thoughts were. Jane didn't know what the state of the hunter, as she called it, was. She didn't know if it had survived its encounter with Jane or not.. There was something about it that just bothered her, she wasn't sure why or maybe she didn't want to know?

**Back on the Space Station:**

The space station was completely now. Not a sign of life was found on the station. Bodies, blood and the remains of any mechs that still roamed around the station lay strewn around the place like something out of a horror film.

In the area where Jane Shepard had blasted the unknown being, there was nothing but debris and fire. Suddenly, the rumble of pieces of the ceiling starting to move echoed around the station. As a hand bust out from the scattered ruins, a hand reached out, almost as if it was trying to grab something, or someone. But after just a few moments the hand balled into a fist in anger.

The hunter lives.

**End of Chapter I**

**Now Naruto will show up in next chapter, I won't spoil anything. ****But for now all I say who are in Naruto's harem for now are**

**Jane Shepard, Kasumi, Miranda, Jack, Dr. Chakwas**

**Later everyone!**


	2. Chapter 2

**Don't own the Naruto series or Mass Effect Series**

**Hello everyone Bunji here, I like to thanks everyone who review this story so far and also Happy New Years yeah I know 11 days late but oh well XD anyway well tell more on this story down below after chapter ends.**

**Chapter II-Forming The Team part 1**

"Shepard I know you've been out of action for two years. But we have some questions we would like to ask you." Miranda Lawson spoke.

"Miranda, Shepard is here. Trust me. The Commander was brought back." Jacob Taylor told Miranda.

"We have to make sure this is Shepard or everything we've done, everything we accomplished, was for nothing." Miranda snapped a glare at Jacob.

"Relax you two. If you want to know if it's the real me then listen to what I remember two years ago." Jane Shepard looked to her right staring out to the window viewing the empty vast of space.

"It's just another routine mission. Why do they always say that before a mission? Of course it's routine…you haven't done anything yet. It's everything that happens along the way, the choices you make, the path choose-that turn the routine into anything but. Of course that's how it started. A routine mission-answering a distress call. And look where that got me." Jane Shepard explained, obviously referring to the last thing that happen before her death.

"We were testing out the Normandy, Captain Anderson's new ship, when the distress call came in. An Alliance patrol on Eden Prime had been attacked. They'd seen something they couldn't explain. And whatever it was…it was massive. I hit the ground with my Lieutenant, Kaiden Alenko-a good kid. Loyal. By the book. With a talent for biotics. We came across the lone survivor of the patrol, Gunnery Chief Ashley Williams. A soldier to the core, Tough. Disciplined. Ready to take on whatever came her way."

"Good enough information you two?" Jane asked Miranda and Jacob.

"I never judge if it wasn't you Shepard. We just had to make sure it was you." Miranda told the red hair Commander.

"I can go on and tell you more if the information you needed isn't enough?" Jane said with a bored stare on her face.

"Aside from Kaiden and Ashley who else do you remember that help you on your journey two years ago Commander?" Miranda asked.

"Ah yes," Jane smiled "Well beside those two, I had a…odd group who became my friends. The first being Garrus, a turian who wanted to help. A top agent of C-Sec, carrying out an investigation on Saren despite orders from his superiors that he shouldn't get involved. Garrus was one of the most trustworthy soldiers I have ever had. When it came to hitting your mark Garrus was the turian for the job. I'm glad I had him."

"Then there was Wrex, biggest, nastiest looking Krogan bounty hunter I'd ever seen. Real hardassed mother-fucker, but it turned out he was more than brute force. It was his Intel that led us to a fugitive with incriminating evidence on Saren. That fugitive turned out to be an energetic little quarian named Tali. A tech expert with a knack for hacking, with her evidence we proved Saren was dirty and needed to be stopped. Crazy teenager with a shotgun and a quarian hatred of Geth? Just what we needed. Another close friend I made on my journey…Liara. An expert on the Protheans. Adept in biotics, when it came to Protheans, Liara just couldn't keep quiet about it. There was no book worm like Liara, although it was kinda funny to tease her." Jane's smile faded as she wonders what has become of her friends she had met as she was dead for two years.

"On Virmire, where you destroyed Saren's cloning facility. You had to leave one of your squad behind to die in that blast." Miranda said.

"Lieutenant Kaiden Alenko was killed in action. It was your call. Why did you leave him behind?" Jacob asked Jane.

The memories of day never faded from Jane's heart.

"I left a close friend to die that day; I didn't do it because I wanted too. I had to save as many people as I could. Kaiden was a soldier and my…friend. He knew what had to be done and gave his life for rest of the team. Without him I couldn't have stopped Saren. He died a hero. Thanks to him, we got everyone else out alive." Jane told the two Cerberus agents as look of anger came across her face.

"I understand, Commander. And I wasn't judging your decision. Everyone knew that cloning facility had to be destroyed." Jacob said.

"Shepard your memory seems solid. There are other tests we really should run-" Before Miranda could finish Jacob cut Miranda off.

"Miranda, the memories are there and I can vouch for Shepard's combat skills personally." Jacob smirked at Miranda. Miranda sighed, but nodded her agreement.

"I suppose you're right. We'll have to wait and see whether The Illusive Man accepts our little test as evidence enough." Miranda said.

"Who's he?" Jane asked.

"You'll see soon enough Shepard." Lawson smiled.

Upon landing at a nearby Cerberus space station. Shepard, Miranda and Jacob departed from their small ship and entered the station. From there Miranda told Shepard to enter a nearby room to greet The Illusive Man who waited for the Commander.

However upon entering the small room. There was a pad on the bottom. Shepard stepped on the pad and she was being scanned by a device. And before her very eyes she saw the image of The Illusive Man before her.

"Commander Shepard." The Illusive Man said warmly. The Illusive Man was relaxing in his chair, enjoying a smoke while having a pleased look on his face.

"Illusive Man. I thought we'd be meeting face-to-face." She said.

"A necessary precaution. Not unusual for people who know what you and I know." He told her.

"You might be the reason I'm still alive, but that doesn't mean I trust you." She said with a bored stare.

"You need to put your personal feelings beside. Humanity is up against the greatest threat of our existence." The Illusive Man frowned.

"The Reapers." Shepard frowned also.

"Good to see your memory's still intact. How are you feeling Shepard?" He asked.

"I was told you made some 'upgrades' while I was asleep you didn't add anything 'good' did you?" Shepard glared at the Illusive Man.

"We needed you to back how you were. Adding a few things to rebuild you was needed. You were quite a mess when we rebuilt you, Shepard. Hope you don't mind few scars, we didn't have time to complete you one hundred percent." He explained. He notices Shepard's odd eye colors.

"Records show you had blue eyes while you work the Alliance. Wearing contact lenses over your natural eyes, I suppose everyone has their reasons." He smirked.

'_Asshole.'_ She thought.

"Cerberus isn't evil as you believe. You and I are on the same side; we just have different methods." He said.

"Cut the crap, why did you bring me back?" Shepard said coldly.

The Illusive man rose up from his chair "We're at war. No one wants to admit it, but humanity is under attack. While you've been sleeping, entire colonies have been disappearing, human colonies. We believe it's someone working for the Reapers, just like Saren was. You've seen it yourself. You bested them all. That is just one reason why you were brought back."

"Why doesn't the Alliance step in do something about it?" She raised an eyebrow.

"After the attack of Sovereign they're rebuilding, still stretched too thin to waste any time on anything Reaper related and willing to blame the abductions on mercs or pirates. Only you know what's really going and will do something about it. You're unique. Not just in ability or what you've experienced, but what you represent. You stood for humanity at a key moment. You're more than a soldier-you're a symbol Shepard. I don't know if the Reapers understand fear, but you killed one. They have to respect that." The Illusive Man told Shepard, a faint smile on his face.

"Geez, you make it sound like I'm somewhat of a God?" Shepard rubbed the back of her head, she didn't believe Cerberus had put that much faith in her.

"Don't let it go to your head. You're still Commander Shepard." He shook his head lightly.

"If what you say is true, if the Reapers are behind this…I'd consider helping you." Shepard closed her eyes while fold her arms over her chest.

"I have a shuttle ready to take you to Freedom's Progress, the latest colony to be abducted. Miranda and Jacob will brief you." The Illusive Man took a seat back down on his chair." He waited for what Shepard had anything else to say.

"Miranda killed Wilson in cold blood. Jacob's a gun for hire. You expect me to trust them?" Shepard open her eyes only to stare with unpleased look.

"Wilson was one of my best agents but he betrayed us. Miranda did exactly what I expected of her. she saved your life in more ways than one. Jacob's a soldier, one of the best. He's never fully trusted me, but he's always been honest about it. You just have to trust them Shepard." He said.

"I still don't like this."She frowned.

"You always have a choice, Shepard. If you don't find any evidence we're both looking for, we can part ways and you go back to your normal life. But go to Freedom's Progress, a favor after what we done for you. It's the least you can do for us." He was right, Shepard owed them her life. Shepard let out a sigh and gave a nod.

'_Something tells me I'm going to find more than just few answers.'_

'_**Upon our journey to Freedom Progress I ran into a familiar face. Tali, my old crew mate and one of my best friends. It seems that Tali and her squad were looking for a quarian by the name of Veetor. Its been two years since I last saw Tali and it must have been quite a shock, judging by how surprised she was to see me. It's good to know those closest to me cared.**_

_**With Tali's help, Miranda, Jacob and I were able to find out what was going on. It seem that the colonies of humans that disappear turned out to be in the hands of a race called The Collectors. If these Collectors were working for the Reapers we needed to act now and right away.**_

_**I let Tali take what was left of her squad and Veetor back to her ship. Veetor have been through a lot seeing the horrors the Collectors have done to the people of Freedom Progress. We return to the space station to inform The Illusive Man what had happened on Freedom Progress and from there our journey truly began.'**_

**Cerberus Space Station:**

"Shepard. Good work on Freedom Progress. The data that Veetor collected didn't give us any information we didn't already know. But we at least we now know who are going after the colonies one by one. The Collectors are behind the abductions." The Illusive Man said.

"Why do I get the feeling you knew that already?" Shepard raised her left eyebrow.

"I had my suspicions, but we needed proof. But thanks to you we now know that rumor is true. The Collectors periodically travel to the Terminus System. When their transactions are complete, they disappear quickly as they arrived, back beyond the unmapped Omega 4 relay." He explained.

"Why the is Omega 4 relay unmapped?" She asked.

"Because no ship has ever returned from it. Our best guess is they are using that location for their hideout. If they can manipulate relays, that's just further evidence of the connection with the Reapers. The Council and Alliance want to believe the Reaper threat died with Sovereign. You and I know better, that was just one Reaper and looked how much damage only one can cause." Shepard agreed with him, what he told her was the truth. One Reaper alone caused so much damage and just think if they had to face ten or one hundred of them?

"If this is going to be a war, I'll need an army. Or a really good team, a large team." She told him.

"Ah. I've already compiled a list of soldiers, scientists and mercenaries. You'll get dossiers on the best of them. Finding them and convincing them to work with you could be challenging, but you're a natural leader Shepard. I'll continue to track the Collectors. When they make their next appearance, I'll notify you and your team, be ready." He explained to Shepard.

"You can keep your list. I want people I can trust-like my old team. You know, the ones who helped me stop Saren and the geth, the ones who helped me blow the fuck out of Virmire, ya know. That team." Shepard told him sarcastically, despite her deadpan expression.

"That was two years ago, much has changed Shepard. While you were being rebuilt, most of your crew has moved on or their allegiances have changed. You having your run in with Tali was unexpected. I need more Intel before I'll commit to that." His information was really starting to piss Jane off.

"Okay, I get it. They're not available." She sweatdropped.

"You're a leader, Shepard. You'll get who you need. But in meantime there's a Galaxy waiting for you. but first two things before you go. First head to Omega and find Mordin Solus. He's a brilliant salarian scientist. Our intelligence suggest he may know how to counteract the Collectors' paralysing seeker swarms." He told her.

"And what's the other thing?" She asked.

"I've found a pilot I think you might like. I hear he's one of the best." The Illusive Man had a smirk on his face as the connection link between the two was finally cut.

"Commander. Just like old times, huh?" A familiar voice spoke. Jane Shepard looked over her right shoulder to see her old friend and former pilot of her ship.

"I can't believe it's you Joker." Jane smiled.

"Look who's talking. I saw you get spaced." Joker smile back.

"I got lucky, falling from space is one hell of a trip. " Jane joked. Her death meant little to her, she was alive now, that was all that mattered.

"It all fell apart without you, Commander. Everything you stirred up, the Council just wanted it gone. Team was broken up, records sealed, and I was grounded. Everything was taken from me. Hell yeah I joined Cerberus." Joker explained to Jane.

"Do you really trust The Illusive Man?" She asked.

"I don't trust anyone who makes more than I do. But they aren't all bad. Saved your life, let me fly." He said with a smile.

"Think we should give him a nickname?" Jane chuckled at Joker's idea.

"T.I.M. sounds about good." She said.

"You think so? I was going to call him Flash-Eyes. Have you seen his eyes? There's something odd about him. Oh, and Commander? Follow me. I got to show you something I know both you and I will like." Jane followed Joker out of the small room to the upper floors where there was a large window. From there Joker waited to see the look on Jane's face upon what she saw behind the large window.

Jane's eyes widen in surprise for what she glaze upon. From behind the large window was a giant hanger which held a copy of Shepard's old spaceship the Normandy.

"They told me last night about it." Joker told Jane.

"I guess we have to give her a name." Jane said.

**Few hours later upon the Normandy:**

"Welcome to the new Normandy Commander." Jacob said.

"It looks almost just like the original." Jane looked around the ship as she was just amazed by what they done with the ship. Though she did notice few new things added to the Normandy 2 she calls it.

"Looking over the dossiers. I'd strongly recommend starting by acquiring Mordin Solus, the salarian professor on Omega. We'll need him to develop that counteract to protect us from the Collectors swarms they been using to capture their prey." Miranda reminded Shepard.

"Yeah, without that countermeasure our ass is grass if ever ran into those Collectors, but fucking remember who is in charge here, cheerleader. My ship, my rules." Jane replied, nodding to the genetically modified human.

"_**Acquiring Professor Solus seem like the most logical place to start." **_A new voice spoke.

"Who said that?!" Jane looked around. Suddenly behind Shepard appeared was an image of a small blue orb.

"_**I am the Normandy's artificial intelligence. The crew like to refer to me as EDI."**_ The A.I introduced itself to Jane.

"Joker won't like this. When someone take control of a ship from him." Jane shook her head.

"_**I do not helm the ship. Mr. Moreau's talents will not go to waste. During combat, I operate the electronic warfare and cyber-warefare suites. Behind that, I cannot interface with the ship's system. I observe and offer analysis and advice. Nothing more." **_EDI Explained.

"The new Normandy has a full crew. They're at their stations waiting your orders. Jacob and I should return to our post. Come find us if you have any questions Commander." Miranda said before departing.

'_And so it begins.'_ Jane thought to herself.

**Somewhere in the Galaxy: Omega**

Omega, built in the mined out husk of a metallic asteroid. Omega, a haven for criminals alike. However, all who live on Omega respect and obey the rule of one woman: an asari by the name of Aria T'Loak. Anyone who disrespects her, or even dares to get in her way meet a sickening end, either quickly or slowly. However there are many things the people of Omega respect and fear Aria for. As wherever she goes her guardian isn't far from behind. On top of a rooftop of a building was a being cast in shadow while looking down upon the lower levels of Omega. Suddenly an incoming radio transmission was heard.

"_**Hey Guardian. You're needed."**_ The voice said over the radio.

The unknown person sighed.

"**What is it? I'm busy hunting, it's much harder to find those bastards. They're like cockroaches now, ever since Archangel showed up. Not that I'm not bitching or anything he's making my job a damn sight easier."** The unknown person said.

"_**Aria needs you. She wants you to greet her new guest that will be arriving soon."**_

"**New guest? It's been awhile since Aria ever had guests. This should be fun. Patch me in, I want to speak with her."** The unknown person said.

After waiting for awhile the unknown person heard Aria's voice asking him what's wrong.

"**Having some guests, huh? It's been awhile, these guest or guests, ya want me to kill them, or play with them?"** He chuckle.

"_**I want to make sure these guests are who the rumors SAY they are. Just make it quick and don't goof around, I know you love to play with your food…Eddie."**_

"**Bah, when it comes to having fun you sure know how to kill it…well unless you're the one playing."** The unknown person laughed.

"_**The guest I am most interested in is female so keep your dick in your pants."**_

"**Relax I'll be a good guardian. Beside if my wife knew I was poking other females beside her and you do you really think I would be here talking to you now?"**

"_**I'll keep that in mind later."**_

"**Well since the cockroaches won't show up, I guess I can kill the boredom by making your guest feel at home. I can't wait to find out who your guests are."** As the shadow cast over the unknown person lifted, he slowly came into full view. The unknown person was a man, wearing a black armor suit with glowing dark blue lines that would glow every five seconds. Before the camera went upward to view his face, from the neck of his armored suit was piece of metal that formed into his mask that covered his face. The helmet the man now wore had two breathing pads on each cheek, while the eyes of the helmet were dark blue.

"**Time to greet our new guest."** The armored man held out his right hand and with a simple twist of his wrist out came a 2 foot long katana blade. As smoke streamed out from the cheeks, the suit suddenly changed, from jet black to crimson red.

**End of Chapter 2**

**From this point, not every word or action will be from the game, I only use this for some parts that all. I skip Freedom's progress mainly because I wanted to get right away to Omega which will be in the next chapter.**

**I skip most of the Shepard's background for this reason so I will introduce the rest of this for when the crew or Naruto ask Jane of her past more which I believe seem useful/needed. **

**Now most of you have question me about the harem Naruto's having and have asked a number of females to join the others in. ****Dr. Chakwas I had no idea she was that old. Her appearance seem a woman in her early 50 or late 40's so I will make her age deage her a bit. **

**And yes Tali is in Naruto's harem. So all of you can stop worrying or asking me about it ok? The rest of who's in the Harem will be shown bit by bit as the story goes on ok everyone? Now Naruto has a wife but I'm not gonna spoil who she is, you all will have to wait to see how it happen and why-evil chuckle-and she isn't from Naruto's world so relax everyone.**

**Well that's all for now everyone see ya!**


	3. Chapter 3

**I don't own Naruto series or Mass Effect**

**Hello everyone Bunji here, sorry for the long hold here. Also warning this chapter isn't betaed my beta for this story is unable to beta for me after a problem that strike him. Now I don't want to hear any you should get a beta or whatever, my beta is out I'm giving him a break, but if anyone want to beta for this story let me know okay?**

**Anyway enjoy!**

**Chapter 3-Forming the Team part 2**

Upon arriving at Omega, Shepard was companied by Miranda and Jacob upon this trip. Since every member Shepard knew was busy with other matters or couldn't be found.

"So this is Omega huh?" Jane said as she looked around her surroundings. The place was huge and very city-like to her point of view.

"Yes, but Omega is a very dangerous place, best to keep our guard up Shepard." Miranda warned Jane.

"The faster we find the Doctor and Archangel the better we can get off this rock." Jacob said.

"Alright then let's see if anyone knows where those two are." Jane told her two squad members.

As they enter through a doorway that lend to what appears to be a small alleyway. Miranda took lend while Jane and Jacob follow her from behind.

'_So this place feels off, feels like there's someone or something watching us.'_ Jane's thoughts were. Jane looked up to see the sky of Omega only to see something in the air floating down above them. Shepard couldn't make out what it was until she saw something shining in its right hand, it was a two foot long katana blade.

The unknown being was dead set on striking Miranda down with its katana blade. Jane acted quickly by the best manner she could. Booting Miranda's big ass!

"Shepard what the hell!" Miranda looked over her right shoulder to see a being in red armor holding a two foot blade sword. The being in red armor paid no mind to Miranda as it was dead set on Jane.

Jane took out her pistol and fired at least three shots at the being in red armor. However the red armored being blocked Jane's shot using its katana.

The red armored being suddenly back flip over Miranda and ran down the alley.

Jane jumped over Miranda and chased after the armored being.

"Come on Miranda get your ass up." Jane yelled as she chased after the armored being. Jacob and Miranda followed after Jane as ran deeper into Omega chasing after the red assassin.

However they lost the trail of their unknown armored stalker.

"Damn where did he go." Jane growled.

"Omega is big he could be anywhere." Miranda said.

"Whoever he is he should know how to run pretty quick." Jacob said.

_'He looks just like that thing from before.'_ Jane thought. Miranda and Jacob notice the worried look in Jane's eyes.

"Commander is everything alright?" Jacob asked Jane, Jane snapped out of it quickly.

"Yeah I'm fine just wonders if any like that will happen again long as we stay here. Let's find what we came for and get the hell of here." Jane told them.

"Agreed." Jacob said.

"Commander," Miranda said as Jane looked at her wondering what she wanted?

"Though you kicked me you save my life there." She told Jane.

"If you're going to say thank you, don't worry about it. Even though we just met I suppose your okay person Miranda. Now can we get going?" Jane said with a stare.

"Yes of course Commander." Miranda nodded.

Jane saw the red assassin from the far corner of another alleyway. Miranda and Jacob also saw him. Thus the team continues to chase down the assassin in red.

"Shepard he's too fast we'll never catch up." Jacob said.

"There's three way slip just up ahead and an old bridge about twenty feet ahead of us." Miranda said while looking at her onmi-tool.

"Okay, Miranda you go west and Jacob you go east I'm going north." Jane said as once the team reached the three way slip. The armored assassin went up north, Jane pushed herself as she catch up with her assassin.

The red assassin looked over its right shoulder and was a bit surprise Jane was catching up with him. Suddenly the armored assassin gain speed.

The armored assassin saw the bridge just up ahead. Just before he was about to reach the bridge Miranda suddenly pop out from a hidden alleyway and was about bash the being's face in. But the armored being slide underneath between Miranda's legs and quickly landed a big spank on her ass.

**"Call me we'll bang ok."** He laughed teasing her. While Miranda bare her teeth while hissing from the painfully ass slap he gave her.

"You let him through your legs and slapped your ass?" Jane deathpan stare at Miranda.

"Oh shut up, where's Jacob?" She asked Miranda.

The two heard the sound of Jacob yelling. They saw Jacob surprise attack the hunter using his biotics to knocked the armored being to a wall.

The armored being shook his head as he was corner by the three.

"Fun's over." Miranda said.

"You're about to find what those who crosses Commander Shepard's path end up too." Jacob told the armored being.

**"Commander Shepard? Ah so your Shepard. The one I heard so much about. As much as this joy to my boss, I'll have to put our little date on hold. I'm late meeting a friend of mine. How about a rain check?"** The armored being said.

"How about I put a bullet in your skull?" Jane aimed her pistol at the assassin.

The armored being chuckled **"How about a FLASHBOMB!"**

Suddenly a bright flash of light came from nowhere blinding their sights as the armored being slide jumped right over them. And ran towards the bridge only to perform a super high jump over the old bridge and landed safety on his two feet.

The armored being right arm transform into a arm canon and blasted the old bridge cutting them off.

**"If ya want to find me again. Go to Afterlife I'll be waiting."** The armored ran off while laughing.

"Whoa that some amazing firepower he was packing." Jacob said.

"Yeah no kidding. I'm going to Afterlife I want to find who that asshole is and make him pay." Jane growl in anger. Jane looked to her right to see Miranda was rubbing her ass.

"What's the matter with you?" Jane raise a brow.

"N-N-nothing." Miranda said as her cheeks glow lightly red.

"You liked it didn't you?" Jane had a big smirked on her face.

"I-I-I DID NOT!" Her face was glowing bright red as Miranda closed her eyes and walked off.

**Afterlife:**

Afterlife one of the most well known clubs in Omega, whenever you wanted a time from reality or just want some time to kill, this was the place for it. But Afterlife didn't like anyone who shows off or think they are better than anyone else.

Jane and her squad arrive at Afterlife as they went up the stairs believing they could find someone who knew where the good Doctor and Archangel was and also find their little red assassin here too.

Going up to the second floor Jane's widen for what she saw waiting there. Shepard did found the one running Omega but also found the red assassin who they lost track of. Jane aimed her handgun at the red assassin who had his back facing Jane.

Upon drawing her gun, Jane, Miranda and Jacob looked to their left and right to see they were surrounded by group of Turian guards who were armed with submachine guns and handguns.

"You can relax Shepard." A female voice said. Shepard looked to see the red assassin took a sidestep to see a light purple colored Asari woman sitting on a large side couch.

"You must be Aria T'Loak." Miranda said.

The Asari woman glared at the three humans. Aria snapped her fingers as her guards lower their weapons and turned away returning to their position. Jane kept her aim on the red assassin.

"You can lower your weapon Shepard. You came here for something didn't you?" Aria said with a bored look on her face. Jane lowered her handgun but kept glaring at the red assassin.

"Care to explain what the hell is that thing!?" Jane asked Aria as she looked at the red assassin.

"This thing is my-" Before she even had the chance finish, the assassin spoke.

"**Her bodyguard, guardian or if a more suitable name her knight, I get the job done when others can't. You stand before the ruler of Omega or rather Queen."** The red Assassin spoke.

"You rule Omega?" Jane asked.

Aria laughed before she stood up before she said proudly.

"I am Omega!" Aria sat back down. She looked at her 'Knight' and jerked her head to the right.

The red Assassin took a bow front of Aria before he performs a back flip down to the lower levels of Afterlife club.

"I take it you sent your pet after us?" Jane asked Aria.

"Call him what you want, he serve me better than any thugs for hired. He did what he was told and now he's going back to what he does best." Jane saw a small smirk came across Aria's face before she frown.

"So Commander Shepard what do you want from me?" She asked.

"How do you know me we never met?" Jane raised an eyebrow.

"Those who don't know Commander Shepard is either dead or live under a rock. We all know what you've done it's big enough for a whole Star system to know in least than an hour." Aria smirked for a moment.

_"**Aria was one mean bitch. She had power and she knew what to do with it. She rule Omega as she saw fit, to her it was one giant playground. Aria informed us the whereabouts Mordin Solus and Archangel."**_

"You can find Mordin to the east near the apartment take the elevator to the lowers floors. As for Archangel, well depenting how long he will last against the Blood Pack, Blue Suns and the Eclipse." Aria told Jane.

"If Archangel is causing you so much damage in the past, why get rid of him now?" Jacob asked Aria.

"Its because he wasn't a big problem until now." Aria explained.

"Your…assassin will take care of the problem?" Miranda asked with a curious looked.

"He won't step in." She told them.

"Why not?" Jane asked.

"Why don't you ask him yourself next time you see him or he see you, now if you're done."

"I should go then." Jane told.

"Yeah you should." Aria said with a long stare.

'_Bitch.'_ Jane thought.

Jane, Miranda and Jacob decide to go and find Mordin first before going to Archangel since he was the closest. The team took the elevators to the lower floors to find Mordin fast, since a rumor that spread about an illness that has been striking the residents of Omega but however, human are immune to the illness. Some of the alien residents believe the humans were behind this and Mordin was helping spread the plague.

"Since this plague doesn't effect humans. We should make this quick Commander who knows what we'll encounter down here." Miranda said.

"True, but if anything or anyone get in my way. I might have to break a bone or two." Jane smirked.

After a few minutes of traveling through a long empty hallway. The team came across a large door that was blocking their path. Miranda used her Omni-tool to hack the door's system to force it open. When the door opened the team eyes widen with shock for what they saw.

It was another long hallway but however, the hallway was filled with bodies as the walls was colored with blood. The bodies were from different race from humans to Turians, Salarians and Batarians and even a Krogan corpse was there.

"My God." Miranda said with look of disgust.

"Poor bastard, I don't see any bullets holes." Jacob said.

"That's because whatever hit them never gave them the chance to fire." Jane touched the blood on the floor. She rubbed her right thumb and index finger together.

"Blood still warm," Jane frown.

"Whoever did this is close by then." Miranda said with an unpleased look.

Suddenly they heard the sound of a person's groaning. Down the hallway they saw a Batarian still alive but wounded. There was a large cut across his chest.

"Hey who did this to you?" Jane asked the Batarian.

**"I don't…need your help human. Your kind is the cause of this plague…"** Batarian cough badly as he was bleeding bad from his wound.

"Shepard he's going to die the wound is too deep." Miranda told Shepard. Shepard used her Omni-tool to use some medic-gel on the Batarian's chest to ease and heal some of the chest wound.

**"You…save…me?"** Batarian look surprise when Jane choose to save him.

"Not all humans are bad. Just because the plague doesn't affect us doesn't mean shit. Now tell us what happen, who did this to you?" Jane asked the Batarian.

**"I don't know…it came from nowhere. It was…a ghost…"** The Batarian coughed.

"A ghost?" Jacob looked confuse.

**"We only heard footsteps then it appeared. It cut through us like butter. I watch my friends were slaughter like sheep…I only survive I guess it only saw me not a threat to it. It went down the hallway downstairs. Ealier I saw a group of Blood Pacts down there…not sure what they got will be enough to deal whatever the hell that thing was."** The Batarian coughed.

"Do you know what it look like?" Jane asked.

**"Covered in red armor that's all I know."** Batarian said.

"Red armor…" Jane frowned.

"You think its Aria's Knight?" Jacob asked.

**"No, it can't be him. He protects Omega it can't be him. That's not how Eddie works."** Batarian cough badly.

"Take it easy. We're going on ahead I'll get help." Jane told the Batarian.

"Who's Eddie?" Miranda asked.

"Must be the 'Knight' name. Let get a move on and Mordin fast." Miranda and Jacob nodded as they left with Shepard in hope of find out just what was going on here?

Jane, Miranda and Jacob enter another room however, this room was bloody just like the hallway awhile back. Jane touched the blood on the ground.

"Blood gone cold." She said with a worry stare.

"Could be this spot could of happen before the hallway slaughter." Jacob said to Jane.

"Maybe," Suddenly the team heard voices from afar. The team slowly walked to a corner that lends to a large open area. Jane from a far a group of Blue Suns Mechs was speaking with Aria's Knight. The red assassin had his back turned on the Blue Suns.

"We grow tired of the bullshit you've been feeding us. Why the hell should we stay off from this area? Everyone getting sick and it's only going to get worst let us pass and we'll find and kill what started this." One of the Blue Suns members spoke.

"**Listen up and listen well kids. Aria told me not to let anyone from Blood Packs, Blue Suns or whatever Gang down here. Listen and turn back or we're going to have a problem."** The Red Assassin spoke.

"What could you do there's thirteen of us and only one you." Another member spoke.

"**If you want to dance that's fine by me, but don't say I didn't give you the chance walking away."** Jane saw with a simply turn of his right wrist a long bladed katana appeared. The Red Assassin quickly grabbed his blade and with one quick slash of his weapon slice through three men with ease.

"**Now you're ten." **He chuckled.

"Shoot him! Shoot him!" The leader of the group yelled.

The remaining members fired their guns at the Red Assassin. However through bullets were being blocked by his katana blade. He went passed them as he sliced his blade through them like a hot knife through butter.

Their blood colored the walls and floors. Their screams were loud but quickly silence.

"W-what are you?" The leader asked the Red Assassin. The Assassin quickly dispose of the remaining men in seconds, leaving the leader corner to a wall. He held his blade against the leader's throat.

"**You're death."** With a quick downward slash the leader didn't even scream as the slash was quick slicing him in two before he even had the chance to scream.

The Red Assassin wiped the blood off his katana and sheath his sword. The Red Assassin turned his back but looked over his right shoulder for a moment before he sighed.

"**You can come out Shepard I know you and your 'friends' were watching."** He said.

Jane, Miranda and Jacob come out walking towards him but kept a safe distance away from him.

"**No close encounter, I thought you wanted to see me face to face?"** The Red Assassin said.

"Not after what I see what you can do." Jane looked around seeing the remains of the corpse of the men he slice to pieces.

"**I guess so, but not the first time I've done something like this before."** He let out a cocky chuckled.

"You seem fine, slaughtering them like sheep." Jacob said with a stare.

"**That wasn't a slaughter. If I was going to slaughter them there would be more blood, more body parts, more pieces to guess what body parts they belongs too."** He told them.

"So your Omega's guardian? I've never heard anyone of your state." Miranda said as she eyed the Red Assassin from head to toe.

'_So this is Jane Shepard, gotta say red fit her well. And her friend also looks hot lovely hips both of them have.'_ He stared at Jane and Miranda.

"How long have you been working for Aria?" Jacob asked Aria's 'Knight'.

"**I don't remember how long, but I've been her 'Knight' for a very long time. I do things others can't and things that could make Aria angry but yet also make her happy."** The Red Knight laughed.

"So you sleep with her?" Jane asked him.

"**Sure why not?" **Again he laughed.

"I hear the only one rule 'Don't fuck with Aria.'" Jane said.

"**True, but I don't fuck with her."** He chuckled.

"I heard your name is Eddie?" Jane glared.

"**That's just a nickname the locals call me. I have many names people call me, Knight, Guardian, Eddie, Omega's Angel or Devil take your pick. But I have only one true name."** He told them.

"And that is?" Miranda asked.

"**If I told I would have to kill you."** His voice darken with threats. He saw how Jane's held her handgun tightly.

"**Just kidding."** He laughed.

"Okay, this guy is nuts Shepard. Don't need to waste time on asking him questions." Jacob told Jane. Jane looked at Aria's 'Knight' she couldn't shake off the disturbed feeling as she stare at the 'Knight' it reminded her of the Hunter on the Space station but he wasn't it, he looked completely different. But Jane still felt fear grip around her heart while staring at him.

"Shepard!" Miranda yelled.

"Huh, what?" Jane snapped out of it.

"Jacob said let's go. We have a mission to do remember?" Miranda said to Jane Shepard. Jane shook her head to shake off the ill feeling.

"Right, let's go." Jane told her teammates.

**"Good luck."** The red assassin said.

Once Shepard, Miranda and Jacob left the area, the red assassin had an incoming call. The person on the other end of the call was a woman.

"**Yeah I'm here what is it?" **he answer.

"_**You should follow them Eddie." **_The woman said on the radio.

"**No their fine by themselves I did what she ask for. And also I'm alone so you call me by real name okay Cort? The rest is up to them. They won't cause too much trouble, but that woman Shepard."**

"_**What about her?"**_

"**She's afraid of me I see it in her eyes."**

"_**But you two never met right?"**_

"**I know, but I wonder if she ran into the ones who stolen my first suit years ago?"**

"_**If so it took a pretty long time for them to find a way to use your suit. It was specially made for you and you alone."**_

"**Yeah, but who knows. For now I'll stay close to them but silence as a shadow."**

"_**Also your wife wanted to know if you're going to be late for dinner again or be on time for once."**_Cort chuckled.

"**You can tell her I'll be late I'm playing guardian again."**

"_**Ok but you know what that means right Naruto?"**_

"**Of course gonna make up during sex. Not that neither of us have a problem with that. But right now I got a job to do." **

**End of chapter 3**

**Now for the subject everyone has been asking me "Bunji why the name Eddie? You have used it for about few times in your stories." The reason why I picked the name Eddie and used it for Naruto's nickname here in this story, because, its the english name for the land of the Uzumaki homeland/village its a shorter name for Uzushiogakure, in english it translate to Land of Eddies/Eddie or Hidden Eddy Village also Eddie is another strange form of whirpool.**

**That's all for now everyone hopefully I'll update sooner later everyone!**


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